Taxonomic assignment report

Department of Agriculture, Fisheries and Forestry logo
Facility Hogwarts
Analyst John Doe
Analysis started 2025-03-19 23:05:04
Analysis completed 2025-03-19 23:05:06
Wall time 0:0:2 hours

Sample details

locus COI
preliminary_id Miridae
taxa_of_interest Lygus pratensis
country Netherlands
host Cut flower Paenonia
sample_id VE24-1079_COI
Query DNA sequence

Result overview

Inconclusive
The analyst should attempt subjective species identification at the genus level.
Reasoning - Flag 1B: 2-3 candidate species matched with high stringency (identity ≥ 98.5%).

Preliminary morphology ID confirmed NA

Inconclusive taxonomic identity (Flag 1B)

Taxa of interest ruled out False

Flag 2A: Taxon of interest NOT detected

Flag 5.1A: The given locus for this taxon is well represented in reference database (>5 entries)

Flag 5.2B: 10-90% of related taxa have reference sequence(s) at the given locus

Analyst evaluation

Identification of candidate species

Flag 1B: The analyst should attempt subjective species identification at the genus level
2-3 candidate species matched with high stringency (identity ≥ 98.5%)

Candidate hits must meet ONE of these criteria:

Minimum alignment length 400bp
Minimum query coverage 85.0%

Candidate hits are then classified as follows:

Classification Alignment identity Number of hits Number of species
STRONG MATCH ≥ 98.5% 11 2
MODERATE MATCH ≥ 93.5% NA NA
NO MATCH < 93.5%

Hits per candidate species (top 10 candidates only)

Species Hits Identity E-value
Orius laevigatus 10 99.1% 0.0
Orius horvathi 1 98.8% 0.0

Analyst evaluation

Taxa of interest

This sections shows the taxa of interest specified by the submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.

Taxon of interest Match rank Match taxon Match species Match accession Match identity
Lygus pratensis - - - - -

See the Database coverage section to see database coverage for taxa of interest.

Reference sequence source diversity

This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.

Analyst evaluation

Independent sources

Flag 4B: Reference sequence sources lack diversity and may therefore be unreliable
Reasoning: Matching sequence records for this species have only 1-5 independent sources (found 5 sources)

5 Independent Sources

The matching reference sequences for this species have been annotated by 5 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
MG007857 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Presence sur l'ile de la Reunion de deux especes de punaises predatrices potentiellement utilisables pour la lutte biologique : Orius naivashae (Poppius 1920) et Cyrtopeltis callosus Odhiambo 1961 (Hemiptera, Heteroptera : Anthocoridae et Miridae) Bull Soc Entomol France 123 (1), 29-42 (2018)
MG007857 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Direct Submission Submitted (27-SEP-2017) CBGP, INRA, 475 avenue campus agropolis. Campus international de baillarguet, Monteffrier sur lez 34980, France
MG007859 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Presence sur l'ile de la Reunion de deux especes de punaises predatrices potentiellement utilisables pour la lutte biologique : Orius naivashae (Poppius 1920) et Cyrtopeltis callosus Odhiambo 1961 (Hemiptera, Heteroptera : Anthocoridae et Miridae) Bull Soc Entomol France 123 (1), 29-42 (2018)
MG007859 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Direct Submission Submitted (27-SEP-2017) CBGP, INRA, 475 avenue campus agropolis. Campus international de baillarguet, Monteffrier sur lez 34980, France
MG007856 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Presence sur l'ile de la Reunion de deux especes de punaises predatrices potentiellement utilisables pour la lutte biologique : Orius naivashae (Poppius 1920) et Cyrtopeltis callosus Odhiambo 1961 (Hemiptera, Heteroptera : Anthocoridae et Miridae) Bull Soc Entomol France 123 (1), 29-42 (2018)
MG007856 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Direct Submission Submitted (27-SEP-2017) CBGP, INRA, 475 avenue campus agropolis. Campus international de baillarguet, Monteffrier sur lez 34980, France
MG007858 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Presence sur l'ile de la Reunion de deux especes de punaises predatrices potentiellement utilisables pour la lutte biologique : Orius naivashae (Poppius 1920) et Cyrtopeltis callosus Odhiambo 1961 (Hemiptera, Heteroptera : Anthocoridae et Miridae) Bull Soc Entomol France 123 (1), 29-42 (2018)
MG007858 False Streito,J.-C.
Fontaine,O.
Atiama,M.
Genson,G.
Pierre,E.
Frago,E.
Nibouche,S.
Direct Submission Submitted (27-SEP-2017) CBGP, INRA, 475 avenue campus agropolis. Campus international de baillarguet, Monteffrier sur lez 34980, France

Source 2

Hit accession Automated Authors Title Journal
FM210187 False Pasquer,F.
Pfunder,M.
Frey,B.
Frey,J.E.
Microarray-based genetic identification of beneficial organisms as a new tool for quality control of laboratory cultures Biocontrol Sci Technol (2010) In press
FM210187 False Pasquer,F. Direct Submission Submitted (08-SEP-2008) Pasquer F., Molecular Diagnostics and Epidemiology, Agroscope changins Waedenswil, Schloss, Postfach 185, 8820/ Waedenswil, SWITZERLAND
FM210184 False Pasquer,F.
Pfunder,M.
Frey,B.
Frey,J.E.
Microarray-based genetic identification of beneficial organisms as a new tool for quality control of laboratory cultures Biocontrol Sci Technol (2010) In press
FM210184 False Pasquer,F. Direct Submission Submitted (08-SEP-2008) Pasquer F., Molecular Diagnostics and Epidemiology, Agroscope changins Waedenswil, Schloss, Postfach 185, 8820/ Waedenswil, SWITZERLAND

Source 3

Hit accession Automated Authors Title Journal
KJ467500 False Pinol,J.
Mir,G.
Gomez-Polo,P.
Agusti,N.
Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods Mol Ecol Resour 15 (4), 819-830 (2015)
KJ467500 False Pinol,J.
Mir,G.
Gomez-Polo,P.
Agusti,N.
Direct Submission Submitted (18-FEB-2014) Entomology, IRTA (Institute for Food and Agricultural Research and Technology), Carretera de Cabrils, Km. 2, Cabrils, Barcelona 08348, Spain

Source 4

Hit accession Automated Authors Title Journal
GQ292147 False Jung,S.
Duwal,R.K.
Lee,S.
COI barcoding of true bugs (Insecta, Heteroptera) Mol Ecol Resour 11 (2), 266-270 (2011)
GQ292147 False Jung,S.H. Direct Submission Submitted (17-JUN-2009) CALS, Insect Biosystematics, Seoul Nat. Univ. 200-6102, Seoul, Korea
GQ292148 False Jung,S.
Duwal,R.K.
Lee,S.
COI barcoding of true bugs (Insecta, Heteroptera) Mol Ecol Resour 11 (2), 266-270 (2011)
GQ292148 False Jung,S.H. Direct Submission Submitted (17-JUN-2009) CALS, Insect Biosystematics, Seoul Nat. Univ. 200-6102, Seoul, Korea

Source 5

Hit accession Automated Authors Title Journal
MG452375 False Erfanfar,D.
Srafrazi,A.
Nouri- Ganbalani,G.
Ostovan,H.
Shojaei,M.
COI-based identification of Orius species (Hemiptera: Anthocoridae) from Iran Unpublished
MG452375 False Erfanfar,D.
Sarafrazi,A.
Direct Submission Submitted (05-NOV-2017) Department of Entomology, Science and Research Branch, Eslamic Azad University, Daneshgah Bulvar, Hesarak, Tehran 14155-4933, Iran

Independent sources

Flag 4B: Reference sequence sources lack diversity and may therefore be unreliable
Reasoning: Matching sequence records for this species have only 1-5 independent sources (found 1 sources)

1 Independent Source

The matching reference sequences for this species have been annotated by 1 independent source(s). A source is considered independent if the author list or publication title is distinct.

Source 1

Hit accession Automated Authors Title Journal
MG452387 False Erfanfar,D.
Srafrazi,A.
Nouri- Ganbalani,G.
Ostovan,H.
Shojaei,M.
COI-based identification of Orius species (Hemiptera: Anthocoridae) from Iran Unpublished
MG452387 False Erfanfar,D.
Sarafrazi,A.
Direct Submission Submitted (05-NOV-2017) Department of Entomology, Science and Research Branch, Eslamic Azad University, Daneshgah Bulvar, Hesarak, Tehran 14155-4933, Iran

Database coverage of target taxa

The target taxa include candidate species, the preliminary morphology ID, and any taxa of interest provided by the submitter. Each of these taxa are independently evaluated against the reference database to determine whether sufficient reference data exists to support identification of the target taxon. Insufficient coverage of a taxon can result in that taxon not be correctly identified as the taxonomic identity of the sample. For example, if the sample is Homo sapiens, but Homo sapiens sequences are not included in the reference database, the analysis will be unable to identity Homo sapiens as the correct taxonomic identity, and will most likely assign the closest relative with reference data as the taxonomic identity.

Analyst evaluation

Database coverage

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus


Database coverage of Orius laevigatus

Flag 5.1A: The reference data supports this taxon well
Reasoning: The given locus for this taxon is well represented in reference database (>5 entries)

19 records

There are 19 sequences in the reference database for Orius laevigatus at the given locus COI.

Map of database coverage

Database coverage of species in genus Orius

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Orius
  • At the target locus COI

Number of GenBank records at locus COI


Database coverage of species in genus Orius that occur in country of origin

Flag 5.3A: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Orius
  • At the target locus COI
  • In the sample country of origin Netherlands

Number of GenBank records at locus COI

Database coverage

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus


Database coverage of Orius horvathi

Flag 5.1A: The reference data supports this taxon well
Reasoning: The given locus for this taxon is well represented in reference database (>5 entries)

6 records

There are 6 sequences in the reference database for Orius horvathi at the given locus COI.

Map of database coverage

Database coverage of species in genus Orius

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Orius
  • At the target locus COI

Number of GenBank records at locus COI


Database coverage of species in genus Orius that occur in country of origin

Flag 5.3A: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Orius
  • At the target locus COI
  • In the sample country of origin Netherlands

Number of GenBank records at locus COI

Database coverage

Flag 5.1NA: This taxon could not be fully assessed
Reasoning: Assessment of related species is only possible for taxa at rank genus/species


Database coverage of Miridae

Flag 5.1NA: This taxon could not be fully assessed
Reasoning: Assessment of related species is only possible for taxa at rank genus/species

NA records

There are NA sequences in the reference database for Miridae at the given locus COI.

Map of database coverage

Database coverage

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus


Database coverage of Lygus pratensis

Flag 5.1A: The reference data supports this taxon well
Reasoning: The given locus for this taxon is well represented in reference database (>5 entries)

54 records

There are 54 sequences in the reference database for Lygus pratensis at the given locus COI.

Map of database coverage

Database coverage of species in genus Lygus

Flag 5.2B: The database has some support for species in this genus
Reasoning: 10-90% of related taxa have reference sequence(s) at the given locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Lygus
  • At the target locus COI

Number of GenBank records at locus COI


Database coverage of species in genus Lygus that occur in country of origin

Flag 5.3A: Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus

/ (%) sequence records were found in the reference database for:

  • Species in the genus Lygus
  • At the target locus COI
  • In the sample country of origin Netherlands

Number of GenBank records at locus COI

Intraspecies diversity

This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.

Analyst evaluation

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The phylogetic tree was constructed with FastME using the Neighbor-Joining method. Multiple-sequence alignment of the candidate reference sequences was performed using MAFFT. The visualization is rendered with TidyTree.

Taxonomy Check

The following resources can be used to ensure that the given taxonomy is legitimate and current.

Taxa Database
General GBIF
General ITIS
Mealybugs & scale ScaleNet database
Thrips Thripswiki
Spider Mites Spider Mites Database
Psocodea (Barklice, Booklice, and Parasitic Lice) Psocodea Species File Online
Orthoptera Orthoptera Species File Online
Drosophilidae TaxoDros
Diptera Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum
Aphids Aphid Species File
Ants AntWeb
AntCat
Lepidoptera (butterflies and moths) The Global Lepidoptera Names Index
Gracillariidae (primitive moths) Global Taxonomic Database of Gracillariidae
Pyralidae (pyralid moths) Global Information System on Pyraloidea
Tortricidae (tortrix moths) Tortricidae Resources on the Net